User guide

User guide

• Installation and Setup
  • Create a Virtual Environment (Recommended)
  • Install JaxDEM from GitHub
  • Install by Cloning (Alternative)
  • Next Steps
• Introduction
  • Initialize the Simulation State
  • Initialize the Simulation System
  • Run the Simulation
  • Saving the Simulation
  • Where to Go Next
• The Simulation State
  • State Creation
  • Understanding Positions: pos, pos_c, and pos_p
  • Particle Sizes: rad and _rad
  • Modifying State Attributes
  • Fixed (Immobile) Particles
  • Identifier Fields
  • Setting Up Connections with bond_id
  • Extending the State
  • Merging Two States
  • Stacking States for Trajectories or Batches
  • Trajectories of Batches
  • Utilities
• The Simulation System
  • System Creation
  • A note on static methods
  • Configuring the System
  • Passing Module Objects Directly
  • Summary: three ways to build a system component
  • Time stepping
  • Trajectory rollout
  • Batched simulations with vmap
  • Deactivating Components
  • Random Number Generation
• The Simulation Domain
  • Domain Creation
  • Common Attributes
  • Free Domain
  • Periodic Domain
  • Reflective Domain
  • Reflect-Sphere Domain
  • apply vs shift
• Integrators and Minimizers
  • Linear vs Rotation Integrators
  • Choosing an Integrator
  • Available Linear Integrators
  • Available Rotation Integrators
  • Deactivating an Integrator
  • Passing Constructor Arguments
  • Minimizers
  • The minimize() Routine
  • The Integration Loop
  • Fixed Particles
• Materials, Matchmakers, and Material Tables
  • Creating Materials
  • Creating a MaterialTable
  • Matchmakers
  • Using Material IDs in a Simulation
  • Default MaterialTable in System.create
• Force Models
  • Selecting a Force Model
  • Available Force Models
  • Materials and Force Requirements
  • Combining Force Models
  • Species-Wise Interactions
• The Force Manager
  • Gravity
  • External Forces
  • External Torques
  • Custom Force Functions
  • Force Function Formats
  • How Forces Are Aggregated
  • Computing Potential Energy
  • Infinite Wall Example
• Colliders
  • Selecting a Collider
  • Available Colliders
  • The Naive Collider
  • The Cell List Collider
  • The Multi-Cell List Collider
  • Neighbor-list creation for all colliders
  • The Neighbor List collider
  • Computing Potential Energy
  • How the Collider Fits in the Step Pipeline
• Checkpoint Save and Load
  • Saving simulation checkpoints
  • Loading latest and specific checkpoints
  • Bonded-force model checkpointing
  • Custom force functions and checkpointing
• VTK Post-Processing and Visualization
  • Basic Usage of VTKWriter
  • Opening the data in ParaView
  • Saving Trajectories directly
• Clumps (Rigid Bodies)
  • The Clump Data Model
  • Creating a Clump Manually
  • Using add_clump()
  • Computing Clump Properties
  • Collision Detection and Clumps
  • clump_id vs bond_id
  • Force Aggregation
  • Running a Simulation with Clumps
  • Integration and Clumps
  • Reflective Domains and Clumps
  • Common Pitfalls
• Deformable Particles
  • Creating a Deformable Particle
  • Passing the Model to the System
  • Coefficient Broadcasting
  • Lazy Array Creation
  • 2D vs 3D Differences
  • The elements_id Field
  • Connectivity Masking
  • Adding and Merging Deformable Particles
  • Batched Simulations with vmap
  • A Note on Edges
  • VTK Output
• Facets (Triangular & Line Boundaries)
  • Internal Representation
  • Creating a Single Facet
  • Creating a Triangular Mesh
  • Dynamic Facet Connection
  • Force Routing & Thickness (Minkowski Sum)
  • VTK Visualization
• Custom Module Registration and System Usage
  • Setup
  • Custom Force Model
  • Custom Domain
  • Custom Collider
  • Custom Integrators
  • Notes on Registration